BioC 2.12: CHECK report for goProfiles on petty

Package: goProfiles

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.22.0.tar.gz

StartedAt: 2013-10-08 22:36:30 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:41:56 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 326.2 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'goProfiles/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'goProfiles' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'goProfiles' can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BioCprobes2Entrez: warning in mget(probeslist, env = myenvir,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'fancyhdr.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [175s/176s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     55.231  0.513  56.176
fisherGOProfiles     15.073  0.218  15.337
mergeProfilesLists   13.422  0.165  13.639
printProfiles        12.516  0.161  12.708
plotProfiles         12.231  0.184  12.425
basicProfile         12.091  0.296  12.544
compSummary          10.415  0.168  10.671
equivalentGOProfiles 10.132  0.087  10.322
compareGOProfiles     9.365  0.105   9.536
contractedProfile     4.932  0.040   5.002
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck/00check.log'
for details.

* installing *source* package 'goProfiles' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (goProfiles)

name	user	system	elapsed
CD4ids	0.041	0.005	0.048
GOTermsList	0.007	0.002	0.009
basicProfile	12.091	0.296	12.544
compSummary	10.415	0.168	10.671
compareGOProfiles	9.365	0.105	9.536
compareGeneLists	55.231	0.513	56.176
compareProfilesLists	0.004	0.005	0.009
contractedProfile	4.932	0.040	5.002
conversionFunctions	0.091	0.010	0.100
drosophila	0.019	0.005	0.024
equivSummary	0.016	0.006	0.022
equivalentGOProfiles	10.132	0.087	10.322
expandedLevel	2.720	0.064	2.806
expandedProfile	1.973	0.019	2.002
fisherGOProfiles	15.073	0.218	15.337
fitGOProfile	0.003	0.004	0.007
hugoIds	0.028	0.004	0.031
mergeProfilesLists	13.422	0.165	13.639
ngenes	4.922	0.044	4.987
omimIds	0.013	0.004	0.017
plotProfiles	12.231	0.184	12.425
printProfiles	12.516	0.161	12.708
prostateIds	0.010	0.004	0.013